Now it is taking 2-3 minutes in booting when it is connected through USB of desktop. BUT it is taking very long time in booting when it is connected through USB of LENEVO G430 laptop. Some time I have to use F4 and F5 buttons for fast booting.

my exp. with running SL6 from an usb has been a nightmare. while running the usb did you yum update at all? i did and evey time after a update it would break. i read somewhere that adding to much to a usb system will cause it to break.